EXACT2: the semantics of biomedical protocols.
EXACT2: the semantics of biomedical protocols.
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DOI：
10.1186/1471-2105-15-s14-s5
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发表时间：
2014
影响因子：
3
通讯作者：
Rudkin BB
中科院分区：
文献类型：
--
作者：
Soldatova LN;Nadis D;King RD;Basu PS;Haddi E;Baumlé V;Saunders NJ;Marwan W;Rudkin BB
实验程序的可靠性和可重复性是科学实践的基石。迫切需要更好地表示生物医学协议，以使其他代理人（人或机器）更好地重现结果。一个框架，确保所有的实验方案的复制所需的信息是必不可少的，以实现再现性。我们开发了本体EXACT 2（EXperimental ACTions），旨在捕获生物医学协议可重复性所需的完整语义。为了构建EXACT 2，我们手动检查了来自生物医学多个领域的数百个已发布和商业生物医学协议。在建立了一个明确的模式，提取所需的信息，我们利用文本挖掘工具，翻译成一个机器的格式协议。我们已经验证了EXACT 2的效用，通过成功处理以前的“看不见的”（不用于建设EXACT 2）协议。本文报告了一个全新的版本EXACT 2，它支持生物医学协议的语义定义表示。通过文本挖掘用例验证了EXACT 2捕获生物医学程序语义的能力。在这个EXACT 2是作为一个参考模型的文本挖掘工具，以确定有关的实验行动，及其属性，在生物医学协议中表示的自然语言。提出了一个基于EXACT 2的框架，用于将生物医学协议翻译为机器可接受的格式。EXACT 2本体论足以以机器可处理的形式记录关于生物医学协议的基本信息。EXACT2定义了实验动作的显式语义，可以被各种计算机应用程序使用。它可以作为一个参考模型，用于将自然语言的生物医学协议翻译成语义定义的格式。
The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable other agents (human or machine) to better reproduce results. A framework that ensures that all information required for the replication of experimental protocols is essential to achieve reproducibility. We have developed the ontology EXACT2 (EXperimental ACTions) that is designed to capture the full semantics of biomedical protocols required for their reproducibility. To construct EXACT2 we manually inspected hundreds of published and commercial biomedical protocols from several areas of biomedicine. After establishing a clear pattern for extracting the required information we utilized text-mining tools to translate the protocols into a machine amenable format. We have verified the utility of EXACT2 through the successful processing of previously 'unseen' (not used for the construction of EXACT2) protocols. The paper reports on a fundamentally new version EXACT2 that supports the semantically-defined representation of biomedical protocols. The ability of EXACT2 to capture the semantics of biomedical procedures was verified through a text mining use case. In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language. An EXACT2-based framework for the translation of biomedical protocols to a machine amenable format is proposed. The EXACT2 ontology is sufficient to record, in a machine processable form, the essential information about biomedical protocols. EXACT2 defines explicit semantics of experimental actions, and can be used by various computer applications. It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.